11a. Creating a new ObjectMap

  1. Choose the Surface Editor from the BioImage Suite main page and a new Surface Editor window will appear.
  2. In the Surface Editor window Choose (File | Standard Images | MNI Colin 1mm Stripped) to load the MNI stripped anatomical image as an underlay.
  3. On the Surface Tab of the Surface Editor Window click the Hide All Button to hide all the spline surface images.
  4. Then click the Image Tab to move between the Surface Editor Window tabs.
  5. At the bottom of the Surface Editor Window, Click the Objectmap/Spline Editor button.  A new Objectmap/Spline Editor Window will appear.
  6. On the new Objectmap/Spline Editor Window click Hide All again to hide all the spline surface images.
  7. On the Objectmap/Spline Editor Window click the Mode button from the Spline Mode to a Brush Size.  The Brush Size desired will depend on the size of the ROI that is being drawn.
  8. In the Objectmap/Spline Editor Window, with the brush mode enabled, the image can be painted with values 1-27. The value "0" is used as an eraser, (i.e. use this to remove voxels from given structures).  The objects 1-27 are shown in the image as the color next to the respective object number  (e.g. object 1 will be shown in red).  The objects 1-8 are shown on the Editor Window itself with the rest of the objects available by clicking the More button.  Choose a color by clicking on it, then move the mouse to the image and click the right mouse button and drag the mouse to draw on the image.   
  9. There are several options to help facilitate drawing the on the anatomical image. To increase the size of the window drag the lower right corner of the window out.   To zoom in on the image, click on the image with the middle button and move the mouse backward (with the button pressed).   
    1. Thresholding - threshoding is very useful to segment different types of tissue.  You can choose a threshold range based on image intensity values and enter them in the boxes next to the Fill In and Fill Out Buttons.  To enable the threshold option, click the "Use Thrshld" checkbutton.  If your threshold range is set properly, you can choose a very large brush size and paint the entire slice (as seen in Figure 11a-II-9a)
      1. Threshold Range 800-2000 will segment out Gray Matter
      2. Threshold Range 2000-5000 will segment out White Matter
    2. Masking - masking percentage allows the user the manipulate the opacity of the objectmap to view the underlying anatomical image.  You can use the slider at the bottom of the Objectmap/Spline Editor Window to manipulate the percentage of mask opacity.
    3. Color Editing - This allows the user to change the color of any of the objects for better viewing purposes.  Click on an object color, then clidk the Edit Color button - a new Color Window will appear for the object number you chose.  You can manipulate the Red, Green, Blue sliders to change the given color, then click OK to accept the changes.  The object number will now appear as the new color.
  10. Once the user has drawn the regions of interest, the objectmap can be saved by going back to the Surface Editor Window an clicking (Objectmap |  Save ObjectMap).  If the user is drawing for an extended period of time, the Autosave can be enabled by the ( Objectmap | AutoSave ) checkbutton on the Surface Editor Window.  The AutoSave option will automatically save the objectmap as objectmapname_autosave.hdr every 2 minutes.  If you press F1 a console window will appear telling you every time the objectmap is saved.
Figure 11a1

Methods used to generate new ObjectMaps using the Surface Editor.

Figure 11a2

Methods used to generate new ObjectMaps using the Surface Editor.